I actually just created 10 "dummy" products, assigned categories, images, prices, etc... did an export, deleted the products, and then imported the original file, and it did not work properly.
It seems to be importing products to sub-categories at random. I am not sure why this is happening. In other words if I have categories:
A
--B
--C
--D
E
--B
--F
--G
H
--B
--C
--I
J
--K
--L
--M
You can see that I have a sub category (, that exists in 3 main categories, it won't put the products that belong in B, in all instances, it will import them into only one, but at random.